Saturday, May 29, 2021

Dark Matter Map Reveals Hidden Bridges Between Galaxies



A new map of dark matter in the local universe reveals several previously undiscovered filamentary structures connecting galaxies. The map, developed using machine learning by an international team including a Penn State astrophysicist, could enable studies about the nature of dark matter as well as about the history and future of our local universe.

Dark matter is an elusive substance that makes up 80% of the universe. It also provides the skeleton for what cosmologists call the cosmic web, the large-scale structure of the universe that, due to its gravitational influence, dictates the motion of galaxies and other cosmic material. However, the distribution of local dark matter is currently unknown because it cannot be measured directly. Researchers must instead infer its distribution based on its gravitational influence on other objects in the universe, like galaxies.

"Ironically, it’s easier to study the distribution of dark matter much further away because it reflects the very distant past, which is much less complex,” said Donghui Jeong, associate professor of astronomy and astrophysics at Penn State and a corresponding author of the study. “Over time, as the large-scale structure of the universe has grown, the complexity of the universe has increased, so it is inherently harder to make measurements about dark matter locally.”

Previous attempts to map the cosmic web started with a model of the early universe and then simulated the evolution of the model over billions of years. However, this method is computationally intensive and so far has not been able to produce results detailed enough to see the local universe. In the new study, the researchers took a completely different approach, using machine learning to build a model that uses information about the distribution and motion of galaxies to predict the distribution of dark matter.

The researchers built and trained their model using a large set of galaxy simulations, called Illustris-TNG, which includes galaxies, gasses, other visible matter, as well as dark matter. The team specifically selected simulated galaxies comparable to those in the Milky Way and ultimately identified which properties of galaxies are needed to predict the dark matter distribution.

“When given certain information, the model can essentially fill in the gaps based on what it has looked at before,” said Jeong. “The map from our models doesn’t perfectly fit the simulation data, but we can still reconstruct very detailed structures. We found that including the motion of galaxies—their radial peculiar velocities—in addition to their distribution drastically enhanced the quality of the map and allowed us to see these details.”

The research team then applied their model to real data from the local universe from the Cosmicflow-3 galaxy catalog. The catalog contains comprehensive data about the distribution and movement of more than 17 thousand galaxies in the vicinity of the Milky Way—within 200 megaparsecs. The resulting map of the local cosmic web is published in a paper appearing online May 26 in the Astrophysical Journal.

The map successively reproduced known prominent structures in the local universe, including the "local sheet”—a region of space containing the Milky Way, nearby galaxies in the “local group,” and galaxies in the Virgo cluster—and the “local void”—a relatively empty region of space next to the local group. Additionally, it identified several new structures that require further investigation, including smaller filamentary structures that connect galaxies.


An international team of researchers has produced a map of the dark matter within the local universe, using a model to infer its location due to its gravitational influence on galaxies (black dots). These density maps—each a cross section in different dimensions—reproduce known, prominent features of the universe (red) and also reveal smaller filamentary features (yellow) that act as hidden bridges between galaxies. The X denotes the Milky Way galaxy and arrows denote the motion of the local universe due to gravity. 


Credit: Hong et. al., Astrophysical Journal

“Having a local map of the cosmic web opens up a new chapter of cosmological study,” said Jeong. “We can study how the distribution of dark matter relates to other emission data, which will help us understand the nature of dark matter. And we can study these filamentary structures directly, these hidden bridges between galaxies.”

For example, it has been suggested that the Milky Way and Andromeda galaxies may be slowly moving toward each other, but whether they may collide in many billions of years remains unclear. Studying the dark matter filaments connecting the two galaxies could provide important insights into their future.

“Because dark matter dominates the dynamics of the universe, it basically determines our fate,” said Jeong. “So we can ask a computer to evolve the map for billions of years to see what will happen in the local universe. And we can evolve the model back in time to understand the history of our cosmic neighborhood.”

The researchers believe they can improve the accuracy of their map by adding more galaxies. Planned astronomical surveys, for example using the James Web Space Telescope, could allow them to add faint or small galaxies that have yet to be observed and galaxies that are further away.

In addition to Jeong, the research team includes Sungwook Hong at the University of Seoul/Korea Astronomy and Space Science Institute in Korea, Ho Seong Hwang at the Seoul National University in Korea, and Juhan Kim at the Korea Institute for Advanced Study. This research was supported in part by the National Research Foundation of Korea funded by the Korean Ministry of Education, the Korean Ministry of Science, the U.S. National Science Foundation, the U.S. National Aeronautics and Space Administration Astrophysics Theory program, and the Center for Advanced Computation at the Korea Institute for Advanced Study.



Contacts and sources:
Gail McCormick 
Penn State
 
  

Three Years Younger in Just Eight Weeks? A New Study Suggests Yes!

A groundbreaking clinical trial shows we can reduce biological age (as measured by the Horvath 2013 DNAmAge clock) by more than three years in only eight weeks with diet and lifestyle through balancing DNA methylation.

A first-of-its-kind, peer-reviewed study provides scientific evidence that lifestyle and diet changes can deliver immediate and rapid reduction of our biological age. Since aging is the primary driver of chronic disease, this reduction has the power to help us live better, longer.



Credit: UCLA

The study, released on April 12, utilized a randomized controlled clinical trial conducted among 43 healthy adult males between the ages of 50-72. The 8-week treatment program included diet, sleep, exercise and relaxation guidance, and supplemental probiotics and phytonutrients, resulting in a statistically significant reduction of biological age--over three years younger, compared to controls.

The study was independently conducted by the Helfgott Research Institute, with laboratory assistance from Yale University Center for Genome Analysis, and the results independently analyzed at McGill University and the National University of Natural Medicine.

The study’s lead author, Kara Fitzgerald ND IFMCP, stated that “the combined intervention program was designed to target a specific biological mechanism called DNA methylation, and in particular the DNA methylation patterns that have been identified as highly predictive of biological age. We suspect that this focus was the reason for its remarkable impact. These early results appear to be consistent with, and greatly extend, the very few existing studies that have so far examined the potential for biological age reversal. And it is unique in its use of a safe, non-pharmaceutical dietary and lifestyle program, control group, and the extent of the age reduction. We are currently enrolling participants for a larger study which we expect will corroborate these findings.”

Leading epigeneticist Moshe Szyf PhD of McGill University and co-author on the study adds, “The uniqueness of Dr Fitzgerald approach is that her trial devised a natural but mechanistic driven strategy to target the methylation system of our body. This study provides the first insight into the possibility of using natural alterations to target epigenetic processes and improve our well being and perhaps even longevity and lifespan.

DNA methylation patterns have become a leading means by which scientists evaluate and track biological aging, a term used to describe the accumulation of damage and loss of function to our cells, tissues and organs. This damage is what drives diseases of aging. “What is extremely exciting,” commented Dr. Fitzgerald, “is that food and lifestyle practices, including specific nutrients and food compounds known to selectively alter DNA methylation, are able to have such an impact on those DNA methylation patterns we know predict aging and age-related disease. I believe that this, together with new possibilities for us all to measure and track our DNA methylation age, will provide significant new opportunities for both scientists and consumers.”

To read the study: https://www.aging-us.com/article/202913

For background information on aging and DNA methylation: https://www.drkarafitzgerald.com/2021/04/13/biological-aging-and-methylation/



Contacts and sources:
Impact Journals LLC


Publication: Potential reversal of epigenetic age using a diet and lifestyle intervention: a pilot randomized clinical trial
Kara N. Fitzgerald, Romilly Hodges, Douglas Hanes, Emily Stack, David Cheishvili, Moshe Szyf, Janine Henkel, Melissa W. Twedt, Despina Giannopoulou, Josette Herdell, Sally Logan, Ryan Bradley.. Aging, 2021; 13 (7): 9419 DOI: 10.18632/aging.202913

Tsimane’s Brains Likely Experience Far Less Atrophy than Westerners as They Age

Despite high levels of inflammation, the Tsimane people in Bolivia are unique for their healthy brains that age more slowly, a USC study finds.

The Tsimane have little or no access to health care but are extremely active and consume a high-fiber diet that includes vegetables, fish and lean meat. 
Photo/Courtesy of the Tsimane Health and Life History Project Team


Ateam of international researchers has found that the Tsimane indigenous people of the Bolivian Amazon experience less brain atrophy than their American and European peers. The decrease in their brain volumes with age is 70% slower than in Western populations. Accelerated brain volume loss can be a sign of dementia.

The study was published Wednesday in The Journal of Gerontology, Series A: Biological Sciences and Medical Sciences.

Although people in industrialized nations have access to modern medical care, they are more sedentary and eat a diet high in saturated fats. In contrast, the Tsimane have little or no access to health care but are extremely physically active and consume a high-fiber diet that includes vegetables, fish and lean meat.
 

The study’s results suggest that the Tsimane’s brains likely experience far less atrophy than Westerners as they age. 


Photo/Courtesy of the Tsimane Health and Life History Project Team

“The Tsimane have provided us with an amazing natural experiment on the potentially detrimental effects of modern lifestyles on our health,” said study author Andrei Irimia, an assistant professor of gerontology, neuroscience and biomedical engineering at the USC Leonard Davis School of Gerontology and the USC Viterbi School of Engineering. “These findings suggest that brain atrophy may be slowed substantially by the same lifestyle factors associated with very low risk of heart disease.”

The researchers enrolled 746 Tsimane adults, ages 40 to 94, in their study. To acquire brain scans, they provided transportation for the participants from their remote villages to Trinidad, Bolivia, the closest town with CT scanning equipment. That journey could last as long as two full days with travel by river and road.

The team used the scans to calculate brain volumes and then examined their association with age for Tsimane. Next, they compared these results to those in three industrialized populations in the U.S. and Europe.

The scientists found that the difference in brain volumes between middle age and old age is 70% smaller in Tsimane than in Western populations. This suggests that the Tsimane’s brains likely experience far less brain atrophy than Westerners as they age; atrophy is correlated with risk of cognitive impairment, functional decline and dementia.

The researchers note that the Tsimane have high levels of inflammation, which is typically associated with brain atrophy in Westerners. But their study suggests that high inflammation does not have a pronounced effect upon Tsimane brains.
The Tsimane: healthy hearts and — new research shows — healthy brain aging

According to the study authors, the Tsimane’s low cardiovascular risks may outweigh their infection-driven inflammatory risk, raising new questions about the causes of dementia. One possible reason is that, in Westerners, inflammation is associated with obesity and metabolic causes. In the Tsimane, however, it is driven by respiratory, gastrointestinal and parasitic infections. Infectious diseases are the most prominent cause of death among the Tsimane.

The Tsimane can serve as a baseline for healthy brain aging.

“Our sedentary lifestyle and diet rich in sugars and fats may be accelerating the loss of brain tissue with age and making us more vulnerable to diseases such as Alzheimer’s,” said study author Hillard Kaplan, a professor of health economics and anthropology at Chapman University who has studied the Tsimane for nearly two decades. “The Tsimane can serve as a baseline for healthy brain aging.”

The indigenous Tsimane people captured scientists’ — and the world’s — attention when an earlier study found them to have extraordinarily healthy hearts in older age. That prior study, published by The Lancet in 2017, showed that Tsimane have the lowest prevalence of coronary atherosclerosis of any population known to science and that they have few cardiovascular disease risk factors. The very low rate of heart disease among the roughly 16,000 Tsimane is very likely related to their pre-industrial subsistence lifestyle of hunting, gathering, fishing and farming.

“This study demonstrates that the Tsimane stand out not only in terms of heart health but brain health as well,” Kaplan said. “The findings suggest ample opportunities for interventions to improve brain health, even in populations with high levels of inflammation.”

In addition to Irimia and Kaplan, study authors include Nikhil N. Chaudhari, David J. Robles, Kenneth A. Rostowsky, Alexander S. Maher, Nahian F. Chowdhury, Maria Calvillo, Van Ngo, Margaret Gatz, Wendy J. Mack and Caleb E. Finch (USC), E. Meng Law (Monash University), M. Linda Sutherland, James D. Sutherland and Gregory S. Thomas (MemorialCare, Fountain Valley, Calif.), Christopher J. Rowan (Renown Regional Medical Center), L. Samuel Wann (Ascension Healthcare), Adel H. Allam (Al-Alzhar University, Egypt), Randall C. Thompson (St. Luke’s Mid America Heart Institute), David E. Michalik (University of California, Irvine), Daniel K. Cummings and Edmond Seabright and Paul L. Hooper (University of New Mexico), Sarah Alami and Michael D. Gurven (University of California, Santa Barbara), Angela R. Garcia and Benjamin C. Trumble (Arizona State University, Tempe) and Jonathan Stieglitz (Institute for Advanced Study, Toulouse, France).

Research funding was provided by the National Institute on Aging at the National Institutes of Health (grant RF1 AG 054442) and the Institute for Advanced Study in Toulouse and the French National Research Agency under the Investments for the Future (Investissements d’Avenir) program (grant ANR-17-EURE-0010).
 


Contacts and sources:
Jenesse Miller 
University of Southern California



 


Microbial Gene Discovery Could Mean Greater Gut Health




 As the owner of a human body, you’re carrying trillions of microbes with you everywhere you go. These microscopic organisms aren’t just hitching a ride; many of them perform essential chemical reactions that regulate everything from our digestion to our immune system to our moods.

One important set of reactions relates to fat absorption via bile acids. Our livers make these acids to help digest fats and fat-soluble vitamins as they travel through the small intestine. Near the end of the small intestine, microbes convert the acids into new forms, which can either be beneficial or harmful.

New research from the University of Illinois identifies the last in a set of microbial genes involved in these conversions.

“Locating these bacterial genes will allow mechanistic studies to determine the effect of bile acid conversion on host health. If we find this is a beneficial reaction, therapeutic strategies can be developed to encourage production of these bile acids in the gastrointestinal tract,” says Jason Ridlon, associate professor in the Department of Animal Sciences at U of I and corresponding author of a new article in Gut Microbes.

Lead researcher Jason Ridlon
Photo by Lauren D. Quinn

Microbes produce enzymes that flip the orientation of three hydroxyl groups on bile acid molecules. Flipping them into different configurations rearranges the acid molecules into forms that can be harmful or beneficial. Ridlon and other scientists had already identified the genes for two of these enzymes, but one was still unknown.

To find the missing gene, Ridlon and his collaborators looked back in time. Previous research links the flipping of a specific hydroxyl group – one attached to a location on the acid molecule known as carbon-12 – with a microbe called Clostridium paraputrificum.

“We knew from literature published a few decades ago what species this function was reported in. We confirmed it in a strain of Clostridium paraputrificum that we have in our culture collection. This function is known to be catalyzed by certain enzymes known as reductases,” Ridlon says.

“Using the genome sequence of Clostridium paraputrificum, we identified all the candidate reductases, engineered the genes into E. coli and determined which reductase was able to flip the polar group on bile acids,” he adds.

The research team then searched for similar sequences in the human microbiome.

“We were able to identify the gene in numerous bacterial species that were previously unknown to have this bile acid metabolizing function. This is helpful for human microbiome researchers because the field is moving towards trying to link function with disease. Now we know the precise DNA sequences that encode an enzyme that flip carbon-12 of bile acids,” Ridlon says.

The researchers haven’t yet figured out if flipping the hydroxyl group at carbon-12 is a good or a bad thing. In the “good” category, the flip may play a role in detoxifying harmful bile acids such as deoxycholic acid (DCA) and lithocholic acid (LCA), chemicals known to damage DNA and cause cancers of the colon, liver, and esophagus. But Ridlon notes that “good vs. bad” framing oversimplifies reality.

“While we tend to think of DCA and LCA as ‘bad,’ the context is very important. Infection by Clostridium difficile (C. diff) seems to correlate with low levels of DCA and LCA, for instance, so these bile acids seem to be protective in preventing unwanted colonizers. Chronic high levels of DCA and LCA due to Western lifestyle are ‘bad,’ however, so it is a balancing act,” he says. “A major goal of this research is trying to establish and maintain a ‘Goldilocks zone’ of bile acids – not too much or too little.”

While there is still more to learn, Ridlon says identifying and characterizing these new microbial genes responsible for bile acid conversion is a major step forward for gut health.

The article, “Completion of the gut microbial epi-bile acid pathway,” is published in Gut Microbes [DOI: 10.1080/19490976.2021.1907271]. Authors include Heidi Doden, Patricia Wolf, Rex Gaskins, Karthik Anantharaman, João Alves, and Jason Ridlon. Funding for this research came from the National Institutes of Health and the U.S. Department of Agriculture.

The Department of Animal Sciences is in the College of Agriculture, Consumer and Environmental Sciences at the University of Illinois.



Contacts and sources:
Jason Ridlon
College of Agriculture, Consumer and Environmental Sciences at the University of Illinois.



  
 
 

The Universe Is Hotter Than Expected, Earth Located in Low Density, Cooler Region

Researchers at the UNIGE have succeeded in reconciling cosmological theory and observations of the Universe by considering that it is hotter than previously thought.

The Andromeda galaxy, our nearest neighbour at 2.5 million lightyears away. This galaxy along with ours and hundreds others make up the Virgo supercluster which is about 100 million lightyears in length

Credit: . © DR

Astrophysicists still encounter various inconsistencies between cosmological theory and measurements made with various research instruments. Four values are particularly problematic: the speed of the expansion of the Universe today, the magnitude of matter density variations within the Universe, and the temperature variations and trajectory of the primordial light of the Universe. By no longer fixing the temperature of this light and the curvature of the Universe in their calculations, researchers at the University of Geneva (UNIGE), Switzerland, have succeeded in reconciling theory with the data. The reason? We live in an under-dense region in the Universe which slightly distorts the calculations and leads to these inconsistencies. These results, to be read in a Letter published in Physical Review D, open up new perspectives for cosmology, which would make it possible to answer many questions that are still pending.

Cosmological theorists are confronted with various inconsistencies between their computational results and satellite measurements. The first inconsistency concerns the speed of the expansion of the Universe. “We can measure this speed either through supernovae – stars that implode at the end of their lives – or through the light of the cosmic microwave background (CMB) – the electromagnetic radiation that is observed throughout the Universe”, explains Benjamin Bose, a researcher in the Department of Theoretical Physics in the Faculty of Science at the UNIGE. But these two measurements give a result that differs by more than 10% which cannot be explained by observational errors. The second inconsistency concerns the magnitude of the variation in the density of the matter in the Universe, which again differs by around 8% if calculated from the CMB or from the galaxies in the local Universe. Finally, the last two inconsistencies are statistical features of the temperature variations and light path of the CMB. In this case, theory fails to match the observations made by scientists.


A simple theory to align the results

Research is still trying to resolve these inconsistencies, albeit with a focus on one issue or the other. Benjamin Bose and Lucas Lombriser, a professor in the Department of Theoretical Physics at the UNIGE, sought to reconcile these four inconsistencies with a single theory, which would not itself introduce numerous other hypotheses to be tested. To do this, they chose to analyse the observational data that produces these inconsistencies by not assuming a particular temperature of the CMB – which is usually considered fixed – and the curvature of the Universe. “By removing these two assumptions, not only do the inconsistencies in the temperature variations of the CMB and its trajectory decrease, but those linked to the speed of the expansion of the Universe today and the spatial differences in the density of matter disappear, with measurements that are in statistical agreement!” Benjamin Bose enthuses. But how can this be explained?


The Earth may be located in a region of low density in the Universe

Lucas Lombriser hypothesised that the Earth is located in an under-dense region within the Universe when compared to the average. “This is why the measurements we make are slightly off, with the temperature of the cosmic microwave background being somewhat higher than the temperature we observe locally”, explains the Genevan professor. This hypothesis is corroborated in particular by measurements made of local galaxies, which would support the idea that the Earth is indeed in a less dense region of the Universe than the average.

According to this cosmological theory, the temperature of light would therefore be higher than that measured with our equipment and used in research. And this difference would affect the calculations and lead to these inconsistencies.

The UNIGE researchers now have to redo their data analysis on the basis that we live in a region of under-density in the Universe. “We show here that we do not need new physics to solve the scientific problems we face. It may just be a matter of taking a new point of view”, concludes Benjamin Bose.


Contacts and sources:
University of Geneva (UNIGE)






Publication: This research is published in Physical Review D
DOI: 10.1103/PhysRevD.103.L081304


Tuesday, May 25, 2021

Out of Africa Migration Was No Great Bottleneck to Human Development Shows Remains of Ice Age Romanian Woman, Predecessor to Modern Europeans

Peştera Muierii 1 is the name given to one of the three individuals whose remains were found in a cave of the same name. Peştera Muierii (roughly translates to women’s cave) is the name of a cave system in Baia de Fier in southern Romania. It is best known for the remains of cave bears and for the 1950s discovery of skulls and other skeletal parts from three females that lived about 35,000 to 40,000 years ago.

For the first time, researchers have successfully sequenced the entire genome from the skull of Peştera Muierii 1, a woman who lived in today’s Romania 35,000 years ago. Her high genetic diversity shows that the out of Africa migration was not the great bottleneck in human development but rather this occurred during and after the most recent Ice Age. This is the finding of a new study led by Mattias Jakobsson at Uppsala University and being published in Current Biology.

Credit: Uppsala University Credit: Mattias Jakobsson

“She is a bit more like modern-day Europeans than the individuals in Europe 5,000 years earlier, but the difference is much less than we had thought. We can see that she is not a direct ancestor of modern Europeans, but she is a predecessor of the hunter-gathers that lived in Europe until the end of the last Ice Age,” says Mattias Jakobsson, professor at the Department of Organismal Biology at Uppsala University and the head of the study.

Very few complete genomes older than 30,000 years have been sequenced. Now that the research team can read the entire genome from Peştera Muierii 1 (see the fact box below), they can see similarities with modern humans in Europe while also seeing that she is not a direct ancestor. In previous studies, other researchers observed that the shape of her cranium has similarities with both modern humans and Neanderthals. For this reason, they assumed that she had a greater fraction of Neanderthal ancestry than other contemporaries, making her stand out from the norm. But the genetic analysis in the current study shows that she has the same low level of Neanderthal DNA as most other individuals living in her time. Compared with the remains from some individuals who lived 5,000 years earlier, such as Peştera Oase 1, she had only half as much Neanderthal ancestry.

The spread of modern humans out of Africa about 80,000 years ago is an important period in human history and is often described as a genetic bottleneck. Populations moved out of Africa and into Asia and Europe. The effects of these migrations can be seen even today. Genetic diversity is lower in populations outside of Africa than in African. That Peştera Muierii 1 has high genetic diversity implies that the greatest loss of genetic diversity occurred during the last Ice Age (which ended about 10,000 years ago) instead of during the out of Africa migration.

The skull of Peştera Muierii 1. Now researchers have successfully sequenced the entire genome from the skull of Peştera Muierii 1, a woman who lived in today's Romania 35,000 years ago. 


Credit: Mattias Jakobsson

“This is exciting since it teaches us more about the early population history of Europe. Peştera Muierii 1 has much more genetic diversity than expected for Europe at this time. This shows that genetic variation outside of Africa was considerable until the last Ice Age, and that the Ice Age caused the decrease in diversity in humans outside of Africa.”

The researchers were also able to follow the genetic variation in Europe over the last 35,000 years and see a clear decrease in variations during the last Ice Age. The reduced genetic diversity has previously been linked to pathogenic variants in genomes being more common among populations outside of Africa, but this is in dispute.

“Access to advanced medical genomics has allowed us to study these ancient remains and even be able to look for genetic diseases. To our surprise, we did not find any differences during the last 35,000 years, even though some individuals alive during the Ice Age had low genetic diversity.

Now we have accessed everything possible from these remains. Peştera Muierii 1 is important from a cultural history perspective and will certainly remain interesting for researchers within other areas, but from a genetic perspective, all the data is now available.”

Svensson E. et al. (2021); Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe, Current Biology, May 18 (11 a.m. ET) DOI: 10.1016/j.cub.2021.04.045, https://www.cell.com/current-biology/fulltext/S0960-9822(21)00592-3

 
 


Contacts and sources:
Mattias Jakobsson, Professor at the Department of Organismal Biology
Uppsala University



 


Fulvic Acid has been shown in studies to improve Blood Glucose levels!

No Link Between Milk and Increased Cholesterol According To New Study Of 2 Million People



Regular consumption of milk is not associated with increased levels of cholesterol, according to new research.

A study published in the International Journal of Obesity looked at three large population studies and found that people who regularly drank high amounts of milk had lower levels of both good and bad cholesterol, although their BMI levels were higher than non-milk drinkers. Further analysis of other large studies also suggests that those who regularly consumed milk had a 14% lower risk of coronary heart disease.

Credit: AshokaJegroo / Wikimedia Commons

The team of researchers took a genetic approach to milk consumption by looking at a variation in the lactase gene associated with digestion of milk sugars known as lactose. The study identified that having the genetic variation where people can digest lactose was a good way for identifying people who consumed higher levels of milk.

Prof Vimal Karani, Professor of Nutrigenetics and Nutrigenomics at the University of Reading said:

“We found that among participants with a genetic variation that we associated with higher milk intake, they had higher BMI, body fat, but importantly had lower levels of good and bad cholesterol. We also found that those with the genetic variation had a significantly lower risk of coronary heart disease. All of this suggests that reducing the intake of milk might not be necessary for preventing cardiovascular diseases.”

The new research was conducted following several contradictory studies that have previously investigated the causal link between higher dairy intake and cardiometabolic diseases such as obesity and diabetes. To account for inconsistencies in sampling size, ethnicity and other factors, the team conducted a meta-analysis of data in up to 1.9 million people and used the genetic approach to avoid confounding.

Even though the UK biobank data showed that those with the lactase genetic variation had 11% lower risk of type 2 diabetes, the study did not suggest that there is any strong evidence for a link between higher milk intake and increased likelihood of diabetes or its related traits such as glucose and inflammatory biomarkers.

Professor Karani said:

“The study certainly shows that milk consumption is not a significant issue for cardiovascular disease risk even though there was a small rise in BMI and body fat among milk drinkers. What we do note in the study is that it remains unclear whether it is the fat content in dairy products that is contributing to the lower cholesterol levels or it is due to an unknown ‘milk factor’”.

The team from the University of Reading, University of South Australia, Southern Australian Health and Medical Research Institute, University College London, and University of Auckland worked together on the study.


Contacts and sources:
Pete Bryant
University of Reading




 


EXPERIENCE OXYGENATION AT THE CELLULAR LEVEL

Origins of Life Researchers Develop a New Ecological Biosignature to Detect Life on Distant Planets

When scientists hunt for life, they often look for biosignatures, chemicals or phenomena that indicate the existence of present or past life. Yet it isn’t necessarily the case that the signs of life on Earth are signs of life in other planetary environments. How do we find life in systems that do not resemble ours?

In groundbreaking new work, a team* led by Santa Fe Institute Professor Chris Kempes has developed a new ecological biosignature that could help scientists detect life in vastly different environments. Their work appears as part of a special issue of the Bulletin of Mathematical Biology collected in honor of renowned mathematical biologist James D. Murray.

Artist's conception of where life might be found on a distant planet. 


Illustration: NASA
 
The new research takes its starting point from the idea that stoichiometry, or chemical ratios, can serve as biosignatures. Since “living systems display strikingly consistent ratios in their chemical make-up,” Kempes explains, “we can use stoichiometry to help us detect life.” Yet, as SFI Science Board member and contributor, Simon Levin, explains, “the particular elemental ratios we see on Earth are the result of the particular conditions here, and a particular set of macromolecules like proteins and ribosomes, which have their own stoichiometry.” How can these elemental ratios be generalized beyond the life that we observe on our own planet?

The group solved this problem by building on two lawlike patterns, two scaling laws, that are entangled in elemental ratios we have observed on Earth. The first of these is that in individual cells, stoichiometry varies with cell size. In bacteria, for example, as cell size increases, protein concentrations decrease, and RNA concentrations increase. The second is that the abundance of cells in a given environment follows a power-law distribution. The third, which follows from integrating the first and second into a simple ecological model, is that the elemental abundance of particles to the elemental abundance in the environmental fluid is a function of particle size.

While the first of these (that elemental ratios shift with particle size) makes for a chemical biosignature, it is the third finding that makes for the new ecological biosignature. If we think of biosignatures not simply in terms of single chemicals or particles, and instead take account of the fluids in which particles appear, we see that the chemical abundances of living systems manifest themselves in mathematical ratios between the particle and environment. These general mathematical patterns may show up in coupled systems that differ significantly from Earth.

Ultimately, the theoretical framework is designed for application in future planetary missions. “If we go to an ocean world and look at particles in context with their fluid, we can start to ask whether these particles are exhibiting a power-law that tells us that there is an intentional process, like life, making them,” explains Heather Graham, Deputy Principal Investigator at NASA’s Lab for Agnostic Biosignatures, of which she and Kempes are a part. To take this applied step, however, we need technology to size-sort particles, which, at the moment, we don’t have for spaceflight. Yet the theory is ready, and when the technology lands on Earth, we can send it to icy oceans beyond our solar system with a promising new biosignature in hand.

Read the paper, "Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications," in the Bulletin of Mathematical Biology (May 18, 2021)

*Christopher Kempes (Santa Fe Institute), Michael Follows (MIT), Hillary Smith (Pennsylvania State University), Heather Graham (NASA Goddard Spaceflight Center), Christopher House (Pennsylvania State University), and Simon Levin (Princeton University, Santa Fe Institute) are co-authors on the paper.



Contacts and sources:
J Marshall
Santa Fe Institute



 


‘Synaptic Transistors’ Conditioned to Learn Similar to Pavlov's Dogs: New Brain-Like Computing Device Simulates Human Learning



Researchers have developed a brain-like computing device that is capable of learning by association. With an array of synaptic transistors, new neuromorphic circuit simulates associative learning. ‘Synaptic transistors’ mimic brain’s plasticity by simultaneously processing, storing data.

Similar to how famed physiologist Ivan Pavlov conditioned dogs to associate a bell with food, researchers at Northwestern Engineering and the University of Hong Kong successfully conditioned their circuit to associate light with pressure.

One of the dogs used by Pavlov
Credit: Wikimedia Commons / Rklawton

The research was published April 30 in the journal Nature Communications.

The device’s secret lies within its novel organic, electrochemical “synaptic transistors,” which simultaneously process and store information just like the human brain. The researchers demonstrated that the transistor can mimic the short-term and long-term plasticity of synapses in the human brain, building on memories to learn over time.

With its brain-like ability, the novel transistor and circuit could potentially overcome the limitations of traditional computing, including their energy-sapping hardware and limited ability to perform multiple tasks at the same time. The brain-like device also has higher fault tolerance, continuing to operate smoothly even when some components fail.


“Although the modern computer is outstanding, the human brain can easily outperform it in some complex and unstructured tasks, such as pattern recognition, motor control and multisensory integration,” said Northwestern’s Jonathan Rivnay, a senior author of the study. “This is thanks to the plasticity of the synapse, which is the basic building block of the brain’s computational power. These synapses enable the brain to work in a highly parallel, fault tolerant and energy-efficient manner. In our work, we demonstrate an organic, plastic transistor that mimics key functions of a biological synapse.”

Jonathan Rivnay

Credit: Northwestern University

Rivnay is an assistant professor of biomedical engineering at Northwestern’s McCormick School of Engineering. He co-led the study with Paddy Chan, an associate professor of mechanical engineering at the University of Hong Kong. Xudong Ji, a postdoctoral researcher in Rivnay’s group, is the paper’s first author.

Problems with conventional computing

Conventional, digital computing systems have separate processing and storage units, causing data-intensive tasks to consume large amounts of energy. Inspired by the combined computing and storage process in the human brain, researchers, in recent years, have sought to develop computers that operate more like the human brain, with arrays of devices that function like a network of neurons.

“The way our current computer systems work is that memory and logic are physically separated,” Ji said. “You perform computation and send that information to a memory unit. Then every time you want to retrieve that information, you have to recall it. If we can bring those two separate functions together, we can save space and save on energy costs.”

Currently, the memory resistor, or “memristor,” is the most well-developed technology that can perform combined processing and memory function, but memristors suffer from energy-costly switching and less biocompatibility. These drawbacks led researchers to the synaptic transistor — especially the organic electrochemical synaptic transistor, which operates with low voltages, continuously tunable memory and high compatibility for biological applications. Still, challenges exist.

“Even high-performing organic electrochemical synaptic transistors require the write operation to be decoupled from the read operation,” Rivnay said. “So if you want to retain memory, you have to disconnect it from the write process, which can further complicate integration into circuits or systems.”
How the synaptic transistor works

To overcome these challenges, the Northwestern Engineering and University of Hong Kong team optimized a conductive, plastic material within the organic, electrochemical transistor that can trap ions. In the brain, a synapse is a structure through which a neuron can transmit signals to another neuron, using small molecules called neurotransmitters. In the synaptic transistor, ions behave similarly to neurotransmitters, sending signals between terminals to form an artificial synapse. By retaining stored data from trapped ions, the transistor remembers previous activities, developing long-term plasticity.

The researchers demonstrated their device’s synaptic behavior by connecting single synaptic transistors into a neuromorphic circuit to simulate associative learning. They integrated pressure and light sensors into the circuit and trained the circuit to associate the two unrelated physical inputs (pressure and light) with one another.

Perhaps the most famous example of associative learning is Pavlov’s dog, which naturally drooled when it encountered food. After conditioning the dog to associate a bell ring with food, the dog also began drooling when it heard the sound of a bell. For the neuromorphic circuit, the researchers activated a voltage by applying pressure with a finger press. To condition the circuit to associate light with pressure, the researchers first applied pulsed light from an LED lightbulb and then immediately applied pressure. In this scenario, the pressure is the food and the light is the bell. The device’s corresponding sensors detected both inputs.

After one training cycle, the circuit made an initial connection between light and pressure. After five training cycles, the circuit significantly associated light with pressure. Light, alone, was able to trigger a signal, or “unconditioned response.”
Future applications

Because the synaptic circuit is made of soft polymers, like a plastic, it can be readily fabricated on flexible sheets and easily integrated into soft, wearable electronics, smart robotics, and implantable devices that directly interface with living tissue and even the brain.

“While our application is a proof of concept, our proposed circuit can be further extended to include more sensory inputs and integrated with other electronics to enable on-site, low-power computation,” Rivnay said. “Because it is compatible with biological environments, the device can directly interface with living tissue, which is critical for next-generation bioelectronics.”

The study, “Mimicking Associative Learning Using an Ion-trapping Non-Volatile Synaptic Organic Electrochemical Transistor,” was supported by the National Science Foundation (award number DMR-1751308), Hong Kong’s General Research Fund (award numbers HKU 17264016 and HKU 17204517), and the National Natural Science Foundation of China.


Contacts and sources:
Amada Morris
Northwestern University

 


Robotic Third Thumb: Can You Grasp the Possibilities?





Using a robotic ‘Third Thumb’ can impact how the hand is represented in the brain, finds a new study led by UCL researchers.

Dani Clode with the Third Thumb

Credit: UCL

The team trained people to use a robotic extra thumb and found they could effectively carry out dextrous tasks, like building a tower of blocks, with one hand (now with two thumbs). The researchers report in the journal Science Robotics that participants trained to use the thumb also increasingly felt like it was a part of their body.

Designer Dani Clode began developing the device, called the Third Thumb, as part of an award-winning graduate project at the Royal College of Art, seeking to reframe the way we view prosthetics, from replacing a lost function, to an extension of the human body. She was later invited to join Professor Tamar Makin’s team of neuroscientists at UCL who were investigating how the brain can adapt to body augmentation.

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Professor Makin (UCL Institute of Cognitive Neuroscience), lead author of the study, said: “Body augmentation is a growing field aimed at extending our physical abilities, yet we lack a clear understanding of how our brains can adapt to it. By studying people using Dani’s cleverly-designed Third Thumb, we sought to answer key questions around whether the human brain can support an extra body part, and how the technology might impact our brain.”

The Third Thumb is 3D-printed, making it easy to customise, and is worn on the side of the hand opposite the user’s actual thumb, near the little (pinky) finger. The wearer controls it with pressure sensors attached to their feet, on the underside of the big toes. Wirelessly connected to the Thumb, both toe sensors control different movements of the Thumb by immediately responding to subtle changes of pressure from the wearer.



Credit: UCL: 

For the study, 20 participants were trained to use the Thumb over five days, during which they were also encouraged to take the Thumb home each day after training to use it in daily life scenarios, totalling two to six hours of wear time per day. Those participants were compared to an additional group of 10 control participants who wore a static version of the Thumb while completing the same training.

During daily sessions in the lab, participants were trained to use the Thumb focusing on tasks that helped increase the cooperation between their hand and the Thumb, such as picking up multiple balls or wine glasses with one hand. They learned the basics of using the Thumb very quickly, while the training enabled them to successfully improve their motor control, dexterity and hand-Thumb coordination. Participants were even able to use the Thumb when distracted – building a wooden block tower while doing a maths problem – or while blindfolded.


Credit: UCL

Designer Dani Clode (UCL Institute of Cognitive Neuroscience and Dani Clode Design), who was part of the core research team, said: “Our study shows that people can quickly learn to control an augmentation device and use it for their benefit, without overthinking. We saw that while using the Third Thumb, people changed their natural hand movements, and they also reported that the robotic thumb felt like part of their own body.”

First author of the study, Paulina Kieliba (UCL Institute of Cognitive Neuroscience) said: “Body augmentation could one day be valuable to society in numerous ways, such as enabling a surgeon to get by without an assistant, or a factory worker to work more efficiently. This line of work could revolutionise the concept of prosthetics, and it could help someone who permanently or temporarily can only use one hand, to do everything with that hand. But to get there, we need to continue researching the complicated, interdisciplinary questions of how these devices interact with our brains.”

Credit: UCL

Before and after the training, the researchers scanned participants’ brains using fMRI, while the participants were moving their fingers individually (they were not wearing the Thumb while in the scanner). The researchers found subtle but significant changes to how the hand that had been augmented with the Third Thumb (but not the other hand) was represented in the brain’s sensorimotor cortex. In our brains, each finger is represented distinctly from the others; among the study participants, the brain activity pattern corresponding to each individual finger became more similar (less distinct).

A week later, some of the participants were scanned again, and the changes in their brain’s hand area had subsided, suggesting the changes might not be long-term, although more research is needed to confirm this.

Paulina Kieliba said: “Our study is the first one investigating the use of an augmentation device outside of a lab. It is the first augmentation study carried over multiple days of prolonged training, and the first to have an untrained comparison group. The success of our study shows the value of neuroscientists working closely together with designers and engineers, to ensure that augmentation devices make the most of our brains’ ability to learn and adapt, while also ensuring that augmentation devices can be used safely.”

Professor Makin added: “Evolution hasn’t prepared us to use an extra body part, and we have found that to extend our abilities in new and unexpected ways, the brain will need to adapt the representation of the biological body.”



Credit: UCL

The researchers, based at UCL and the University of Oxford, were supported by the European Research Council, Wellcome and the Sir Halley Stewart Trust.


Contacts and sources:
Chris Lane
University College London






Publication: Robotic hand augmentation drives changes in neural body representation.
Paulina Kieliba, Danielle Clode, Roni O. Maimon-Mor, Tamar R. Makin. Science Robotics, 2021; 6 (54): eabd7935 DOI: 10.1126/scirobotics.abd7935


Nanocrystals Harvest Light with "Energy Transfer Efficiency of over 96%

Inspired by nature, researchers at Pacific Northwest National Laboratory (PNNL), along with collaborators from Washington State University, created a novel material capable of capturing light energy. This material provides a highly efficient artificial light-harvesting system with potential applications in photovoltaics and bioimaging.

The research provides a foundation for overcoming the difficult challenges involved in the creation of hierarchical functional organic-inorganic hybrid materials. Nature provides beautiful examples of hierarchically structured hybrid materials such as bones and teeth. These materials typically showcase a precise atomic arrangement that allows them to achieve many exceptional properties, such as increased strength and toughness.

PNNL materials scientist Chun-Long Chen, corresponding author of this study, and his collaborators created a new material that reflects the structural and functional complexity of natural hybrid materials. This material combines the programmability of a protein-like synthetic molecule with the complexity of a silicate-based nanocluster to create a new class of highly robust nanocrystals. They then programmed this 2D hybrid material to create a highly efficient artificial light-harvesting system.

“The sun is the most important energy source we have,” said Chen. “We wanted to see if we could program our hybrid nanocrystals to harvest light energy—much like natural plants and photosynthetic bacteria can—while achieving a high robustness and processibility seen in synthetic systems.” The results of this study were published May 14, 2021, in Science Advances.
 
Materials scientist Chun-Long Chen finds inspiration for new materials in natural structures. 
(Photo by Andrea Starr | Pacific Northwest National Laboratory)

Big dreams, tiny crystals

Though these types of hierarchically structured materials are exceptionally difficult to create, Chen’s multidisciplinary team of scientists combined their expert knowledge to synthesize a sequence-defined molecule capable of forming such an arrangement. The researchers created an altered protein-like structure, called a peptoid, and attached a precise silicate-based cage-like structure (abbreviated POSS) to one end of it. They then found that, under the right conditions, they could induce these molecules to self-assemble into perfectly shaped crystals of 2D nanosheets. This created another layer of cell-membrane-like complexity similar to that seen in natural hierarchical structures while retaining the high stability and enhanced mechanical properties of the individual molecules.

“As a materials scientist, nature provides me with a lot of inspiration” said Chen. “Whenever I want to design a molecule to do something specific, such as act as a drug delivery vehicle, I can almost always find a natural example to model my designs after.”

POSS-peptoid molecules self-assemble into rhomboid-shaped nanocrystals.

 (Illustration by Stephanie King | Pacific Northwest National Laboratory)

Designing bio-inspired materials

Once the team successfully created these POSS-peptoid nanocrystals and demonstrated their unique properties including high programmability, they then set out to exploit these properties. They programmed the material to include special functional groups at specific locations and intermolecular distances. Because these nanocrystals combine the strength and stability of POSS with the variability of the peptoid building block, the programming possibilities were endless.

Once again looking to nature for inspiration, the scientists created a system that could capture light energy much in the way pigments found in plants do. They added pairs of special “donor” molecules and cage-like structures that could bind an “acceptor” molecule at precise locations within the nanocrystal. The donor molecules absorb light at a specific wavelength and transfer the light energy to the acceptor molecules. The acceptor molecules then emit light at a different wavelength. This newly created system displayed an energy transfer efficiency of over 96%, making it one of the most efficient aqueous light-harvesting systems of its kind reported thus far.

POSS-peptoid nanocrystals form a highly efficient light-harvesting system that absorbs exciting light and emits a fluorescent signal. This system can be used for live cell imaging.
 (Illustration by Chun-Long Chen and Yang Song | Pacific Northwest National Laboratory)

Demonstrating the uses of POSS-peptoids for light harvesting

To showcase the use of this system, the researchers then inserted the nanocrystals into live human cells as a biocompatible probe for live cell imaging. When light of a certain color shines on the cells and the acceptor molecules are present, the cells emit a light of a different color. When the acceptor molecules are absent, the color change is not observed. Though the team only demonstrated the usefulness of this system for live cell imaging so far, the enhanced properties and high programmability of this 2D hybrid material leads them to believe this is one of many applications.

“Though this research is still in its early stages, the unique structural features and high energy transfer of POSS-peptoid 2D nanocrystals have the potential to be applied to many different systems, from photovoltaics to photocatalysis,” said Chen. He and his colleagues will continue to explore avenues for application of this new hybrid material.

Other authors of this study include: James De Yoreo, Mingming Wang, Shuai Zhang, and Xin Zhang from PNNL and Song Yang and Yuehe Lin from Washington State University. Shuai Zhang, James De Yoreo, and Chun-Long Chen are also affiliated with the University of Washington. This work was supported by the U.S. Department of Energy Basic Energy Sciences program as part of the Center for the Science of Synthesis Across Scales, an Energy Frontier Research Center located at the University of Washington.


Contacts and sources:
Sarah Wong
DOE/Pacific Northwest National Laboratory


Publication: Programmable two-dimensional nanocrystals assembled from POSS-containing peptoids as efficient artificial light-harvesting systems.
Mingming Wang, Yang Song, Shuai Zhang, Xin Zhang, Xiaoli Cai, Yuehe Lin, James J. De Yoreo, Chun-Long Chen. Science Advances, 2021; 7 (20): eabg1448 DOI: 10.1126/sciadv.abg1448


Solar Geoengineering May Be Surprisingly Effective in Alleviating Impacts of Global Warming on Crops

Solar geoengineering — putting aerosols into the atmosphere to reflect sunlight and reduce global warming — is not a fix-all for climate change but it could be one of several tools to manage climate risks. A growing body of research has explored the ability of solar geoengineering to reduce physical climate changes. But much less is known about how solar geoengineering could affect the ecosystem and, particularly, agriculture.

Now, research from the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) finds that solar geoengineering may be surprisingly effective in alleviating some of the worst impacts of global warming on crops.

Maize crop in rural India

The research, a collaboration with the Norwegian Research Centre and the Bjerknes Centre for Climate Research, the Norwegian University of Science and Technology, the National Center for Atmospheric Research in Boulder, Seoul National University and the Chinese Academy of Sciences, is published in Nature Food.

“Research on solar geoengineering must address whether or not it is effective at reducing human impacts of climate change,” said David Keith, the Professor of Applied Physics at SEAS and Professor of Public Policy at the Harvard Kennedy School. “Our paper helps fill that gap by using the best crop model yet embedded in a climate model to examine the potential impact of solar geoengineering on agricultural yields.”

The team looked at three types of solar geoengineering — stratospheric aerosol injection, marine sky brightening, and cirrus cloud thinning — and their impact on the global yield of maize, sugarcane, wheat, rice, soy and cotton in a business-as-usual future where emissions continue at their current levels.

In such a future, the most effective way to protect crops against the worst effects of global climate change is to reduce the surface temperature. The researchers found that all three potential solar geoengineering methods have a strong cooling effect that would benefit crop yields.

Previous research suggested that cooling temperatures brought on by stratospheric aerosol injection may also lead to less rainfall, which could result in yield loss for rainfed crops. But these studies didn’t look at one of the most important ecological factors in crop transpiration and productivity — humidity.

“Relative humidity or vapor pressure deficit has stronger control on plant water use and crop productivity than precipitation,” said Yuanchao Fan, a Fellow in the Harvard Solar Geoengineering Research Program and first author of the paper. “We found that in a cooler world under multiple scenarios, except cirrus cloud thinning, there will be higher relative humidity, which will alleviate water stress for rainfed crops. Our model shows that the change in precipitation resulting from all three solar geoengineering methods would, in fact, have very little effect on crops.”





The researchers compared how agricultural productivity is affected by solar geoengineering and emissions reductions. The researchers found that while emissions reductions have strong cooling and humidity benefits, they may have a smaller benefit for crop yields than solar geoengineering because the reduction of CO2 fertilization reduces the productivity of most crops compared with solar geoengineering that achieves the same temperature reduction. The finding highlights the need to combine emissions reductions with other tools, including increasing the use of nitrogen fertilization and changes to land use.

“Climate risks cannot be resolved with any single tool; even if emissions were eliminated tomorrow the world’s most vulnerable will still suffer from climate change,” said Keith. “Policymakers need to consider how emissions cuts might be supplemented by specific local adaptations to help farmers reduce the impacts of climate on agriculture, and by global actions such as carbon removal and solar geoengineering.”

The research with co-authored by Jerry Tjiputra , Helene Muri, Danica Lombardozzi, Chang-Eui Park  and Shengjun Wu.

The research was supported in part by Harvard University’s Solar Geoengineering Research Program.



Contacts and sources:
Leah Burrows
Harvard John A. Paulson School of Engineering and Applied Sciences

Publication: Solar geoengineering can alleviate climate change pressures on crop yields.
Yuanchao Fan, Jerry Tjiputra, Helene Muri, Danica Lombardozzi, Chang-Eui Park, Shengjun Wu, David Keith. Nature Food, 2021; 2 (5): 373 DOI: 10.1038/s43016-021-00278-w

Monday, May 24, 2021

Total Deaths Due to COVID-19 Underestimated by 20% in US Counties



More than 15 months into the pandemic, the U.S. death toll from COVID-19 is nearing 600,000. But COVID-19 deaths may be underestimated by 20 percent, according to a new, first-of-its-kind study from the School of Public Health, the University of Pennsylvania, and the Robert Wood Johnson Foundation.


Credit: Boston University School of Medicine

Published in the journal PLOS Medicine, the study uses data from the National Center for Health Statistics (NCHS) and the Centers for Disease Control and Prevention (CDC) to estimate the number of deaths in 2,096 counties from January to December 2020 above what would be expected in a normal year, or “excess deaths.” For every 100 excess deaths directly attributed to COVID-19, there were another 20 excess deaths not attributed to COVID-19. In other words, 20 out of every 120 excess deaths, or 17 percent, were not directly attributed to COVID.

The researchers found that the proportion of these excess deaths not directly attributed to COVID-19 was higher in counties with lower average socioeconomic status and less formal education, as well as in counties located in the South and West. Counties with more non-Hispanic Black residents—who were already at high risk of dying directly from COVID-19—also reported a higher proportion of excess deaths not assigned to COVID-19.

“Our findings suggest that the impact of the COVID-19 pandemic on mortality has been substantially underestimated in many communities across the US,” says study lead author Andrew Stokes, assistant professor of global health. “Several factors, including severe testing shortages, overwhelmed health care systems, and a lack of familiarity with the clinical manifestations of COVID-19 has likely led to significant underreporting of COVID-19 on death certificates, especially early in the pandemic. Official COVID-19 death tallies also fail to capture the pandemic’s profound social and economic consequences, including the downstream effects of interruptions in receiving health care, loss of employment, evictions, and social isolation and loneliness.”

In addition to deaths directly from the coronavirus that were not recorded as such, some of the excess deaths are likely from indirect consequences of the COVID crisis, including fear of going to the hospital for another condition, or any number of issues caused or exacerbated by the toll that COVID has taken on the economy and on mental health.

“Counties with high levels of COVID-19 mortality also had exceptionally high levels of mortality in 2020 from other causes of death. This result suggests that the epidemic is responsible for many more deaths than are attributed to COVID-19 alone,” says study senior author Samuel H. Preston, professor of sociology at the University of Pennsylvania.

“Racial and socioeconomic inequities in U.S. mortality have widened significantly as a result of the COVID pandemic, especially when considering total excess deaths. To protect public health, policymakers must act decisively to address structural racism and reduce income inequality,” says study co-author Dielle Lundberg, a research fellow in the Department of Global Health at SPH.

Overall, the study makes clear that county-level measures of direct COVID-19 mortality were not accurate measures of excess mortality in many US counties.

“A more complete accounting of COVID-19 deaths in local communities using excess deaths could lead to increased public awareness and vaccine uptake, particularly in areas where the official death counts suggested the pandemic had a limited impact,” Stokes says.

The study was also co-authored by Jacob Bor, assistant professor of global health and epidemiology at SPH, Irma T. Elo of the University of Pennsylvania, and Katherine Hempstead of the Robert Wood Johnson Foundation, and was funded by the Robert Wood Johnson Foundation.



Contacts and sources:
Michelle Samuels
Boston University School of Medicine



Publication: COVID-19 and excess mortality in the United States: A county-level analysis.
Andrew C. Stokes, Dielle J. Lundberg, Irma T. Elo, Katherine Hempstead, Jacob Bor, Samuel H. Preston.PLOS Medicine, 2021; 18 (5): e1003571 DOI: 10.1371/journal.pmed.1003571





The True Origin of Watermelon

Just in time for picnic-table trivia, a new study published in the Proceedings of the National Academy of Sciences rewrites the origins of domesticated watermelons.

Using DNA from greenhouse-grown plants representing all species and hundreds of varieties of watermelon, scientists discovered that watermelons most likely came from wild crop progenitors in northeast Africa.

The study corrects a 90-year-old mistake that lumped watermelons into the same category as the South African citron melon. Instead, researchers, including a first author now at Washington University in St. Louis, found that a Sudanese form with non-bitter whitish pulp, known as the Kordofan melon (C. lanatus), is the closest relative of domesticated watermelons.

The genetic research is consistent with newly interpreted Egyptian tomb paintings that suggest the watermelon may have been consumed in the Nile Valley as a dessert more than 4,000 years ago.

In the inset, a painting shows the distinctive stripes of a watermelon-like fruit.
 (Courtesy of the researchers)

“Based on DNA, we found that watermelons as we know them today — with sweet, often red pulp that can be eaten raw — were genetically closest to wild forms from west Africa and northeast Africa,” said Susanne S. Renner, honorary professor of biology in Arts & Sciences at Washington University.
 

Renner is an evolutionary biologist who recently joined Washington University after 17 years working as a professor at Ludwig Maximilian University in Munich, Germany, where she also served as the director of the Munich Botanical Garden and Munich herbarium.

Her lab has long focused on honey melons and cucumbers, but for the past 10 years she has turned to watermelons and bitter gourds.

The genetic information published in the new study — completed with colleagues from the U.S. Department of Agriculture in Ithaca, New York; the Royal Botanic Gardens, Kew in London; and the University of Sheffield — could be useful for developing a more disease-resistant watermelon crop, Renner said.

“Today’s watermelon comes from a very small genetic stock and is highly susceptible to diseases and insect pests, including various mildews, other fungi, viruses and nematodes [worms],” Renner said. “So far, we found variation in three disease resistance genes between the Kordofan melon and the domesticated watermelon. Breeders might use these and other insights from the genome.”

Watermelon on a mobile fruit shop in Hurghada, Egypt.
(Photo: Shutterstock)

But some of the greatest takeaways from this study, Renner said, are related to the mobility of people and their cultural connections.

“It was the Egyptian tomb paintings that convinced me that the Egyptians were eating cold watermelon pulp,” Renner said. “Otherwise, why place those huge fruits on flat trays next to grapes and other sweet fruits?”

“Melons, cucumbers and watermelons were domesticated several times” across human history, she said. “But to place these domestications in space and name is much more difficult than I thought 10 to 15 years ago. DNA from ancient seeds is already beginning to help.”


Contacts and sources:
Talia Ogliore
Washington University in St. Louis

Publication: A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons.
Susanne S. Renner, Shan Wu, Oscar A. Pérez-Escobar, Martina V. Silber, Zhangjun Fei, Guillaume Chomicki. Proceedings of the National Academy of Sciences, 2021; 118 (23): e2101486118 DOI: 10.1073/pnas.2101486118


Surprisingly High Levels of Mercury in Greenland Glacier Meltwater

An aerial view of Nuup Kangerlua (fjord) and the glaciers that feed meltwater into it. This fjord receives approximately 20 cubic kilometers of meltwater from the ice sheet every year (equivalent to 8 million Olympic sized swimming pools of water). 


Photo courtesy of Jade Hatton/University of Bristol.

New research shows that concentrations of the toxic element mercury in rivers and fjords connected to the Greenland Ice Sheet are comparable to rivers in industrial China, an unexpected finding that is raising questions about the effects of glacial melting in an area that is a major exporter of seafood.

“There are surprisingly high levels of mercury in the glacier meltwaters we sampled in southwest Greenland,” said Jon Hawkings, a postdoctoral researcher at Florida State University and and the German Research Centre for Geosciences. “And that’s leading us to look now at a whole host of other questions such as how that mercury could potentially get into the food chain.”

The study was published today in Nature Geoscience.

The international study began as a collaboration between Hawkings and glaciologist Jemma Wadham, a professor at the University of Bristol’s Cabot Institute for the Environment.

Initially, researchers sampled waters from three different rivers and two fjords next to the ice sheet to gain a better understanding of meltwater water quality from the glacier and how nutrients in these meltwaters may sustain coastal ecosystems.

One of the elements they measured for was the potentially toxic element mercury, but they had no expectation that they would find such high concentrations in the water there.

Typical dissolved mercury content in rivers are about 1 – 10 ng L-1 (the equivalent of a salt grain-sized amount of mercury in an Olympic swimming pool of water). In the glacier meltwater rivers sampled in Greenland, scientists found dissolved mercury levels in excess of 150 ng L-1, far higher than an average river. Particulate mercury carried by glacial flour (the sediment that makes glacial rivers look milky) was found in very high concentrations of more than 2000 ng L-1.

With any unusual finding, the results raise more questions than answers. Researchers are unclear if the mercury levels will dissipate farther away from the ice sheet and whether this “glacier” derived mercury is making its way into the aquatic food web, where it can often concentrate further.

“We didn’t expect there would be anywhere near that amount of mercury in the glacial water there,” said Associate Professor of Earth, Ocean and Atmospheric Science Rob Spencer. “Naturally, we have hypotheses as to what is leading to these high mercury concentrations, but these findings have raised a whole host of questions that we don’t have the answers to yet.”

Fishing is Greenland’s primary industry with the country being a major exporter of cold-water shrimp, halibut and cod.

“We’ve learned from many years of fieldwork at these sites in Western Greenland that glaciers export nutrients to the ocean, but the discovery that they may also carry potential toxins unveils a concerning dimension to how glaciers influence water quality and downstream communities, which may alter in a warming world and highlights the need for further investigation,” Wadham said.

The finding underscores the complicated reality of rapidly melting ice sheets across the globe. About 10 percent of the Earth’s land surface is covered by glaciers, and these environments are undergoing rapid change as a result of rising temperatures. Scientists worldwide are working to understand how warming temperatures — and thus more rapidly melting glaciers — will affect geochemical processes critical to life on Earth.

“For decades, scientists perceived glaciers as frozen blocks of water that had limited relevance to the Earth’s geochemical and biological processes,” Spencer said. “But we’ve shown over the past several years that line of thinking isn’t true. This study continues to highlight that these ice sheets are rich with elements of relevance to life.”

Hawkings also said it was worth noting that this source of mercury is very likely coming from the Earth itself, as opposed to a fossil fuel combustion or other industrial source. That may matter in how scientists and policymakers think about the management of mercury pollution in the future.

“All the efforts to manage mercury thus far have come from the idea that the increasing concentrations we have been seeing across the Earth system come primarily from direct anthropogenic activity, like industry,” Hawkings said. “But mercury coming from climatically sensitive environments like glaciers could be a source that is much more difficult to manage.”

Other scientists contributing to the study come from an international team based in the United States (USGS, Woods Hole Oceanographic Institute, University of California Santa Cruz, Brigham Young University) United Kingdom (University of Bristol, University of Glasgow), Czechia (Charles University), Norway (UiT The Arctic University of Norway, UiO University of Oslo), Greenland (Greenland Climate Research Centre) and the Netherlands (Royal Netherlands Institute of Sea Research).

The fieldwork was supported by grants through the Leverhulme Trust and the UKRI’s Natural Environment Research Council. Jon Hawkings was also supported by a European Commission Horizon 2020 Marie Sklodowska-Curie Actions Fellowship. Part of the research was conducted at the Florida State University-headquartered National High Magnetic Field Laboratory, funded by the National Science Foundation and the state of Florida.






Contacts and sources:
Florida State University


Publication: . Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet.
Jon R. Hawkings, Benjamin S. Linhoff, Jemma L. Wadham, Marek Stibal, Carl H. Lamborg, Gregory T. Carling, Guillaume Lamarche-Gagnon, Tyler J. Kohler, Rachael Ward, Katharine R. Hendry, Lukáš Falteisek, Anne M. Kellerman, Karen A. Cameron, Jade E. Hatton, Sarah Tingey, Amy D. Holt, Petra Vinšová, Stefan Hofer, Marie Bulínová, Tomáš Větrovský, Lorenz Meire, Robert G. M. Spencer. Large subglacial source of mercury from the southwestern margin of the Greenland Ice Sheet. Nature Geoscience, 2021; DOI: 10.1038/s41561-021-00753-w






Hazards of Earth's Largest Volcano




Researchers find that a large earthquake could set off eruption of Hawaii’s Mauna Loa volcano

 Scientists from the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science analyzed ground movements measured by Interferometric Synthetic Aperture Radar (InSAR) satellite data and GPS stations to precisely model where magma intruded and how magma influx changed over time, as well as where faults under the flanks moved without generating significant earthquakes. The GPS network is operated by the U.S. Geological Survey’s Hawaii Volcano Observatory.

Mauna Loa volcano: The largest volcano on Earth (volume and area) gently defines the horizon from the southern flank of Mauna Kea.
Credit: Wikimedia Commons / Joe Parks from Berkeley, CA

“An earthquake of magnitude-6 or greater would relieve the stress imparted by the influx of magma along a sub-horizontal fault under the western flank of the volcano,” said Bhuvan Varugu, a Ph.D. candidate at the UM Rosenstiel School and lead author of the study. “This earthquake could trigger an eruption.”

The researchers found that during 2014-2020 a total of 0.11 kilometers3 of new magma intruded into a dike-like magma body located under and south of the summit caldera, with the upper edge at 2.5 - 3 kilometers depth beneath the summit. They were able to determine that in 2015 the magma began expanding southward, where the topographic elevation is lower and the magma had less work to do against the topographic pressure. After the magma flux waned in 2017, the inflation center returned to its previous 2014-2015 horizontal position. Such changes of a magma body have never been observed before.

“At Mauna Loa, flank motion and eruptions are inherently related,” said Varugu. “The influx of new magma started in 2014 after more than four years of seaward motion of the eastern flank - which opened up space in the rift zone for the magma to intrude.”

Standing 9 kilometers tall from the base on the seafloor to the summit, Mauna Loa is the largest volcano on Earth.

Image: USGS


The researchers also found that there was movement not associated with an earthquake along a near-horizontal fault under the eastern flank, however, no movement was detected under the western flank. This led the researchers to conclude that an earthquake under the western flank is due. Motions along near-horizontal faults under the flanks are essential features of long-term volcano growth.

Will the volcano erupt in the near future? “If magma influx continues it is likely, but not required,” says Varugu. “The topographic load is pretty heavy, the magma could also propagate laterally through the rift zone”.

“An earthquake could be a game changer,” said Falk Amelung, a professor at the UM Rosenstiel School’s Department of Marine Geosciences and senior author of the study. “It would release gases from the magma comparable to shaking a soda bottle, generating additional pressure and buoyancy, sufficient to break the rock above the magma.”

According to the researchers there are many uncertainties. Though the stress that was exerted along the fault is known, the magnitude of the earthquake will also depend on the size of the fault patch that will actually rupture. Additionally, there are no satellite data available to determine movements prior to 2002.

“It is a fascinating problem,” said Amelung, “We can explain how and why the magma body changed during the past six years. We will continue observing and this will eventually lead to better models to forecast the next eruption site.”

Standing 9 kilometers tall from the base on the seafloor to the summit, Mauna Loa is the largest volcano on Earth. In the 1950 eruption, it took only three hours for the lava to reach the Kona coast. Such rapid flows would leave very little time to evacuate people in the path of its lava. Another large eruption of Mauna Loa occurred in 1984.

The combination of earthquakes and eruptions is nothing unusual. The 1950 eruption was preceded by a magnitude 6.3 earthquake three days prior, and was followed by a magnitude 6.9 earthquake more than a year later. The 1984 eruption was preceded by a magnitude 6.6 earthquake 5 months prior.

The satellite data were acquired by the Italian Cosmo-Skymed satellites in the framework of the Geohazard Supersites and Natural Laboratories (GSNL) initiative of the Group on Earth Observation (GEO), an international umbrella organization to enhance the use of Earth Observation for societal benefits. Several space agencies pool their satellite resources to enable new studies of hazardous volcanoes. Other volcano supersites include the Icelandic, Ecuadorian and New Zealand volcanoes as well as Italy’s Mt. Etna.

The study, titled “Southward growth of Mauna Loa’s dike‐like magma body driven by topographic stress” was published in May 2021 in Nature Scientific Reports. Funding was provided by NASA research grant #NNX15AQ20G to the University of Hawaii and the University of Miami Rosenstiel School of Marine and Atmospheric Science.






Contacts and sources:
Diana Udel
University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science